Software Name Version Classification XDSdata reduction PHENIXrefinement PDB_EXTRACT3.15 data extraction XSCALEdata scaling PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 4egtResolution : 1.95→19.798 Å / SU ML : 0.23 / Cross valid method : FREE R-VALUE / σ(F) : 1.36 / Phase error : 23 / Stereochemistry target values : MLRfactor Num. reflection % reflection Rfree 0.2124 4160 5 % Rwork 0.1798 79014 - obs 0.1814 83174 99.65 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODELDisplacement parameters Biso max : 141.55 Å2 / Biso mean : 25.8415 Å2 / Biso min : 5.71 Å2 Refinement step Cycle : final / Resolution : 1.95→19.798 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 9659 0 27 901 10587 Biso mean - - 29.71 30.48 - Num. residues - - - - 1327
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.005 9960 X-RAY DIFFRACTION f_angle_d0.981 13677 X-RAY DIFFRACTION f_chiral_restr0.039 1536 X-RAY DIFFRACTION f_plane_restr0.005 1814 X-RAY DIFFRACTION f_dihedral_angle_d11.044 3386
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A5900 X-RAY DIFFRACTION 7.499 TORSIONAL1 2 B5900 X-RAY DIFFRACTION 7.499 TORSIONAL1 3 C5900 X-RAY DIFFRACTION 7.499 TORSIONAL1 4 D5900 X-RAY DIFFRACTION 7.499 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 30
Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.9499-1.9721 0.3745 138 0.3105 2624 2762 98 1.9721-1.9953 0.32 134 0.2902 2534 2668 98 1.9953-2.0196 0.3234 138 0.2818 2625 2763 99 2.0196-2.0451 0.2921 138 0.2671 2617 2755 99 2.0451-2.072 0.3068 136 0.2592 2593 2729 100 2.072-2.1003 0.286 138 0.2356 2626 2764 100 2.1003-2.1303 0.2493 139 0.2191 2649 2788 100 2.1303-2.1621 0.2714 137 0.2089 2601 2738 100 2.1621-2.1958 0.2499 141 0.2043 2671 2812 100 2.1958-2.2318 0.2616 137 0.214 2606 2743 100 2.2318-2.2702 0.2799 138 0.2297 2621 2759 100 2.2702-2.3114 0.2532 137 0.209 2610 2747 100 2.3114-2.3558 0.2256 139 0.2018 2635 2774 100 2.3558-2.4038 0.2612 138 0.2046 2629 2767 99 2.4038-2.456 0.2629 139 0.1976 2631 2770 100 2.456-2.513 0.2448 138 0.1963 2631 2769 100 2.513-2.5757 0.2503 139 0.193 2636 2775 100 2.5757-2.6452 0.2143 139 0.1917 2629 2768 100 2.6452-2.7229 0.2532 138 0.187 2635 2773 100 2.7229-2.8105 0.2009 140 0.1892 2646 2786 100 2.8105-2.9107 0.2126 137 0.1812 2619 2756 100 2.9107-3.0268 0.2051 139 0.1723 2637 2776 100 3.0268-3.164 0.18 139 0.1628 2644 2783 100 3.164-3.3301 0.2154 140 0.1606 2651 2791 100 3.3301-3.5376 0.1712 140 0.1552 2659 2799 100 3.5376-3.809 0.1924 140 0.1471 2652 2792 100 3.809-4.189 0.146 140 0.1329 2657 2797 100 4.189-4.7877 0.1364 139 0.1257 2646 2785 100 4.7877-6.004 0.1514 141 0.1396 2685 2826 100 6.004-19.7985 0.1639 144 0.1528 2715 2859 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 40) Hide large table ID L11 (°2 )L12 (°2 )L13 (°2 )L22 (°2 )L23 (°2 )L33 (°2 )S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2 )T12 (Å2 )T13 (Å2 )T22 (Å2 )T23 (Å2 )T33 (Å2 )Origin x (Å)Origin y (Å)Origin z (Å)1 2.6155 4.2208 2.8365 6.8396 4.5791 3.0791 -0.6427 0.4227 0.0446 -0.7936 0.0497 0.0374 0.4943 0.0153 0.6117 0.3866 0.0203 0.0197 0.3147 -0.0179 0.3416 23.6857 -129.7578 174.272 2 0.1765 0.2327 0.0881 1.9828 0.1361 0.8535 -0.0475 -0.0404 -0.0414 -0.025 0.0766 0.0301 -0.0272 0.0242 -0.0411 0.158 0.0174 0.0073 0.1959 -0.0199 0.3341 27.6437 -122.3926 186.6333 3 3.8227 -1.8916 -2.4996 8.2405 6.0518 8.9751 -0.1074 -0.3162 0.1206 -0.6337 -0.0281 0.2223 -0.7526 0.2751 0.129 0.175 0.0125 -0.0757 0.2049 -0.0135 0.3826 33.5878 -103.881 186.797 4 0.4533 -0.5089 -0.697 4.0891 0.2656 3.4406 -0.0314 -0.4162 0.4655 0.2665 0.0064 -0.2643 0.0039 0.0585 0.0775 0.1859 -0.0106 0.0108 0.2013 -0.0427 0.3763 37.4272 -98.5938 201.7994 5 4.9863 -0.0742 -0.2193 2.3007 2.4585 2.6266 -0.2542 0.2339 0.9545 -0.6748 -0.3449 0.4058 -1.0742 0.2165 0.5282 0.3211 0.0193 -0.0856 0.2419 0.022 0.3467 23.7515 -103.2743 185.23 6 1.2502 0.1007 0.0091 1.2977 -0.2056 1.0916 -0.0082 -0.1447 0.0669 0.0648 -0.0443 0.0748 -0.072 -0.0843 0.0369 0.1688 0.0225 -0.0043 0.1816 -0.0421 0.2494 36.0933 -105.1858 199.1837 7 1.1571 0.6763 0.1554 2.1107 0.1945 0.5563 0.0023 -0.1216 0.0154 0.1081 -0.0286 0.1434 -0.0155 -0.0715 0.0339 0.1505 0.0259 0.0179 0.1689 -0.0202 0.2103 32.9187 -118.546 196.5051 8 3.9978 -0.7209 4.4236 1.7224 -1.2517 6.9998 -0.0247 0.1657 -0.3442 0.1462 0.0858 -0.1698 -0.0209 0.3058 -0.0612 0.1569 0.0006 0.0321 0.1499 -0.0314 0.3206 34.5437 -125.0694 188.6511 9 1.294 -0.0448 0.7555 0.6719 0.4738 1.9058 -0.0476 -0.0708 -0.1555 -0.0179 0.0047 0.1573 0.0373 -0.2503 0.0357 0.1755 -0.0144 0.0093 0.2127 -0.0068 0.4042 20.898 -133.3111 184.3648 10 2.7445 1.0454 -0.5558 2.4949 0.6576 3.7135 0.0129 -0.0266 -0.2269 0.2049 -0.0559 0.2092 0.2384 -0.0933 0.0175 0.1842 0.0004 0.0098 0.1322 0.0026 0.3186 24.202 -139.8721 183.9318 11 6.659 -0.8723 2.0271 1.366 2.3472 6.1967 0.1748 -0.0515 0.2567 0.1725 -0.3319 0.3441 0.4564 -0.8081 0.1654 0.1933 -0.0485 0.0291 0.2572 0.0462 0.2674 37.1362 -117.034 168.3076 12 0.7998 -0.141 1.5258 2.9599 -1.2437 3.1207 0.0774 -0.0153 -0.0806 0.0887 -0.1366 -0.0754 -0.02 0.0058 0.0691 0.1191 -0.0116 0.0092 0.1773 -0.013 0.2423 48.2191 -117.9502 168.751 13 5.9727 0.0219 2.703 0.7354 -0.8218 2.1411 0.0642 -0.23 -0.2425 0.0627 -0.0785 -0.2203 -0.0805 -0.0242 0.0082 0.1432 0.0139 0.0378 0.1719 0.0188 0.1985 59.3032 -111.4058 192.247 14 6.5121 3.9991 1.24 4.931 1.8108 6.5366 0.3683 -0.6016 -1.3468 0.3479 -0.4945 0.3307 1.0713 0.0094 0.0948 0.3301 0.0281 -0.0224 0.2215 0.0808 0.503 57.9653 -126.8285 182.7396 15 0.8737 0.0035 -0.0284 0.8867 -0.0746 1.6216 -0.0524 -0.0615 -0.0157 -0.0081 0.0278 -0.0441 -0.0252 0.0225 0.0245 0.1481 0.0103 -0.0244 0.1644 -0.0052 0.2876 58.561 -109.7488 187.176 16 0.7683 0.2683 0.8353 0.0312 0.2917 3.3305 -0.0249 -0.0361 0.1255 -0.0644 0.0308 0.0205 -0.2111 -0.0081 -0.0073 0.1619 -0.0003 0.0119 0.1544 0.0119 0.2636 50.8595 -108.3764 173.0142 17 3.041 1.1612 0.4787 7.409 -0.3325 3.3355 0.2907 1.3169 -1.0728 -2.0644 0.2845 1.8185 0.9461 -1.9892 -0.7141 0.5979 -0.0505 -0.1779 0.7251 -0.0767 0.5638 37.6529 -97.3059 179.2237 18 4.9568 1.0494 -0.2169 2.8929 -1.9374 8.1206 -0.1199 -0.1847 0.689 -0.1126 0.114 0.5882 -0.5107 -0.3037 0.0171 0.073 0.0273 -0.0528 0.252 0.0229 0.3182 42.5178 -107.9222 171.2425 19 1.148 0.5914 0.2397 2.751 -0.9404 2.2552 0.0347 0.0401 -0.0367 -0.1329 -0.0382 0.2635 0.0574 -0.2014 0.0052 0.1548 0.0147 -0.0066 0.2166 -0.0348 0.2552 39.8123 -117.3334 158.886 20 4.9542 -0.237 -0.0038 8.8015 -0.6957 4.908 0.0211 0.3073 0.1224 -0.0092 -0.106 -0.1916 0.1739 -0.297 0.0641 0.1533 -0.0121 -0.0333 0.2443 -0.0247 0.1897 38.468 -116.5369 150.7228 21 9.5392 1.8672 5.8028 2.3912 0.3167 3.865 -0.4644 0.4542 0.5159 -0.5112 -0.2509 0.3526 -0.0556 0.129 0.7702 0.3641 0.084 -0.0536 0.229 -0.0291 0.3726 -1.409 -138.8065 113.7978 22 0.2018 -0.273 0.5092 2.6009 -0.485 1.1349 -0.0526 -0.0084 -0.0145 0.0123 0.0056 0.0962 -0.0617 -0.1118 0.0351 0.1262 -0.0083 0.0275 0.2073 -0.058 0.3246 0.7095 -131.1782 126.3619 23 4.0777 -4.7466 -4.1291 7.5849 6.9155 7.5335 0.3249 -0.1035 -0.0631 -1.1234 -0.4001 0.228 -0.7715 -0.0683 0.1314 0.2003 -0.0023 -0.0045 0.242 -0.0535 0.3531 6.5103 -112.2448 127.3278 24 1.8241 0.5859 0.8101 1.8074 -0.0373 2.0469 -0.0582 -0.1105 0.3181 0.0918 -0.0249 0.3461 -0.1716 0.0288 0.0988 0.1375 0.0082 0.0365 0.1977 -0.064 0.3577 5.7073 -111.4428 137.7169 25 2.4456 3.6218 -1.529 8.0475 -2.4512 1.3286 0.0868 -0.2191 0.0473 0.0978 -0.1832 0.1197 -0.1452 -0.0151 0.0863 0.1275 0.0034 -0.0171 0.1872 -0.0603 0.2592 14.0164 -111.7775 137.1859 26 1.4798 0.6964 0.3495 1.1987 0.386 0.6408 0.0111 -0.2155 0.1447 0.1182 -0.0859 0.1471 0.0274 -0.1461 0.0835 0.1532 -0.0078 0.0233 0.1929 -0.0365 0.2677 4.8961 -119.5345 139.3516 27 5.403 2.262 2.2726 1.399 0.7074 1.8852 -0.105 -0.1723 -0.3788 0.0652 0.012 0.1538 0.0191 -0.1011 0.1385 0.1537 -0.0121 0.0124 0.1358 -0.0391 0.2703 8.3396 -135.4658 134.6099 28 0.0418 0.303 0.1467 2.3987 -0.3103 2.4113 0.0835 -0.033 -0.1699 -0.1317 0.0574 0.2332 0.1433 -0.3204 -0.0869 0.1335 -0.0112 0.0251 0.1853 -0.0329 0.3177 2.3244 -133.7512 124.3988 29 0.4393 -0.2374 -0.4145 2.4495 0.6843 2.0802 -0.0253 0.0156 -0.2273 -0.0114 -0.0549 0.4606 0.155 -0.183 0.0396 0.1614 -0.0456 0.0144 0.1913 -0.0187 0.3877 -3.2536 -144.3282 125.6619 30 5.2906 1.6835 -3.0526 3.649 -0.7026 7.5931 -0.0777 0.0128 0.0679 0.0606 0.1146 0.3256 0.3701 -0.3413 -0.0212 0.187 -0.0198 0.0198 0.1187 -0.0273 0.2505 -3.783 -148.9871 122.1906 31 6.7662 -3.7083 1.6835 7.482 -1.8513 6.333 0.4308 -0.0195 0.6485 -0.1019 -0.6084 -0.06 0.705 -0.1942 0.1603 0.2415 0.003 -0.0324 0.2701 0.0104 0.3539 8.6596 -132.2681 102.8859 32 0.2851 0.2133 0.4249 1.7152 0.0512 2.5555 -0.0177 0.0445 0.0585 -0.0487 -0.0808 0.0256 -0.0964 -0.1374 0.0996 0.1218 0.0083 0.0077 0.1854 -0.0069 0.2647 19.8454 -125.4693 110.1752 33 5.9433 -2.4031 6.8664 3.1788 -2.8024 7.8977 0.45 -0.4686 -0.281 -0.1078 -0.185 -0.4646 0.7414 -0.4159 -0.3429 0.2023 -0.0349 0.0103 0.2221 0.0098 0.2631 25.3403 -129.4817 128.3203 34 2.1644 0.7352 0.5756 4.1291 2.7779 5.5419 0.002 -0.1457 0.0686 0.1155 -0.0565 -0.195 -0.2258 0.3074 0.0123 0.1232 -0.0246 -0.021 0.1433 0.0188 0.2603 35.6586 -116.5713 136.209 35 4.7263 5.8041 2.4092 7.1111 2.826 8.1886 -0.118 -0.3859 -0.8713 -0.0533 0.0373 -0.5419 0.8051 -0.6311 -0.0486 0.2164 -0.0069 -0.0055 0.1986 0.0675 0.3914 30.9322 -136.0802 124.0953 36 0.8735 -0.3589 0.2995 0.9693 -0.0169 1.3471 -0.0195 0.0039 -0.0742 0.0322 -0.0269 -0.0991 0.0018 0.0319 0.0576 0.1214 -0.0158 -0.0094 0.1328 0.0189 0.2515 31.3563 -119.0155 129.1321 37 1.5411 0.3185 -0.4267 0.8896 1.5876 3.5319 0.0143 -0.0026 0.1594 -0.2397 -0.0387 -0.0087 -0.2363 -0.0757 0.0051 0.1868 0.0183 -0.012 0.1458 0.033 0.2397 23.3244 -115.7013 112.4793 38 1.8831 0.2494 1.0444 1.6629 0.4146 2.2661 -0.0726 0.1237 0.0917 -0.2154 -0.0928 0.1763 -0.261 -0.2145 0.1088 0.1663 0.0576 -0.0182 0.1875 -0.0351 0.2377 15.4801 -125.3907 102.7116 39 4.456 2.9575 -3.6407 7.7057 -2.2709 5.048 0.1535 0.4522 0.7126 -0.135 -0.2538 0.7679 -0.835 -0.3397 0.1014 0.3636 0.0722 -0.1067 0.2916 0.0025 0.2972 13.9727 -112.5481 100.291 40 4.4492 1.5034 -2.0631 2.672 0.5707 4.083 -0.183 0.262 0.3733 -0.179 0.105 0.2807 -0.2405 -0.3178 0.0664 0.2467 0.0672 -0.0788 0.3022 -0.0286 0.2122 11.5504 -124.6272 92.8096
Refinement TLS group Show large table (6 x 40) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 (chain A and resid 237:243)A237 - 243 2 X-RAY DIFFRACTION 2 (chain A and resid 244:290)A244 - 290 3 X-RAY DIFFRACTION 3 (chain A and resid 291:299)A291 - 299 4 X-RAY DIFFRACTION 4 (chain A and resid 300:324)A300 - 324 5 X-RAY DIFFRACTION 5 (chain A and resid 325:331)A325 - 331 6 X-RAY DIFFRACTION 6 (chain A and resid 332:410)A332 - 410 7 X-RAY DIFFRACTION 7 (chain A and resid 411:475)A411 - 475 8 X-RAY DIFFRACTION 8 (chain A and resid 476:500)A476 - 500 9 X-RAY DIFFRACTION 9 (chain A and resid 501:545)A501 - 545 10 X-RAY DIFFRACTION 10 (chain A and resid 546:569)A546 - 569 11 X-RAY DIFFRACTION 11 (chain B and resid 237:257)B237 - 257 12 X-RAY DIFFRACTION 12 (chain B and resid 258:290)B258 - 290 13 X-RAY DIFFRACTION 13 (chain B and resid 291:319)B291 - 319 14 X-RAY DIFFRACTION 14 (chain B and resid 320:330)B320 - 330 15 X-RAY DIFFRACTION 15 (chain B and